rs10088180

chr8-18370607-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000523491.1(NATP):n.1A>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.649 in 153,810 control chromosomes in the GnomAD database, including 33,032 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.65 (33002 hom., cov: 32)
  • Exomes 𝑓: 0.15 (30 hom.)
• Consequence: NATP ENST00000523491.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.53

Genes affected

NATP (HGNC:15): (N-acetyltransferase pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NATP	ENST00000523491.1	n.1A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99457 AN: 151962 Hom.: 32992 Cov.: 32

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.651

GnomAD4 exome AF: 0.147 AC: 254 AN: 1730 Hom.: 30 Cov.: 0 AF XY: 0.178 AC XY: 174 AN XY: 980

Gnomad4 AFR exome AF: 0.125

Gnomad4 AMR exome AF: 0.0603

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0116

Gnomad4 SAS exome AF: 0.0932

Gnomad4 FIN exome AF: 0.199

Gnomad4 NFE exome AF: 0.219

Gnomad4 OTH exome AF: 0.343

GnomAD4 genome AF: 0.654 AC: 99508 AN: 152080 Hom.: 33002 Cov.: 32 AF XY: 0.646 AC XY: 48006 AN XY: 74344

Gnomad4 AFR AF: 0.650

Gnomad4 AMR AF: 0.533

Gnomad4 ASJ AF: 0.684

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.661

Gnomad4 FIN AF: 0.656

Gnomad4 NFE AF: 0.703

Gnomad4 OTH AF: 0.646

Alfa AF: 0.677 Hom.: 13191

Bravo AF: 0.641

Asia WGS AF: 0.502 AC: 1746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
Cadd	Benign	13
Dann	Benign	0.59

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10088180; hg19: chr8-18228116;